1 Find variable genes

2 PCA

3 UMAP

plot_grid(ncol = 2, DimPlot(alldata, reduction = "umap", group.by = "orig.ident", shuffle = TRUE) + 
            NoLegend() + NoAxes(), 
          DimPlot(alldata, reduction = "umap", group.by = "Type", label = TRUE, shuffle = TRUE) + 
            NoLegend() + NoAxes(),
          DimPlot(alldata, reduction = "umap", group.by = "Treatment", shuffle = TRUE) + 
            theme(legend.position = "bottom") + NoAxes())

FeaturePlot(alldata, reduction = "umap", features = c("Ptprc","Epcam"), 
    order = T, slot = "data", combine = T)

FeaturePlot(alldata, reduction = "umap", features = c("Ptprc"), 
    order = T, slot = "data", combine = T, split.by = "Type")

FeaturePlot(alldata, reduction = "umap", features = c("Epcam"), 
    order = T, slot = "data", combine = T, split.by = "Type")

sessionInfo()
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS/LAPACK: /Users/jenfra/miniconda3/envs/singlecell/lib/libopenblasp-r0.3.15.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_3.3.6      cowplot_1.1.1      sp_1.5-0           SeuratObject_4.1.0
## [5] Seurat_4.1.1      
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15            colorspace_2.0-3      deldir_1.0-6         
##   [4] ellipsis_0.3.2        ggridges_0.5.3        rstudioapi_0.13      
##   [7] spatstat.data_2.2-0   farver_2.1.0          leiden_0.3.9         
##  [10] listenv_0.8.0         ggrepel_0.9.1         fansi_1.0.3          
##  [13] codetools_0.2-18      splines_4.0.5         cachem_1.0.6         
##  [16] knitr_1.37            polyclip_1.10-0       jsonlite_1.8.0       
##  [19] ica_1.0-2             cluster_2.1.2         png_0.1-7            
##  [22] rgeos_0.5-9           uwot_0.1.11           shiny_1.7.2          
##  [25] sctransform_0.3.3     spatstat.sparse_2.1-1 compiler_4.0.5       
##  [28] httr_1.4.2            assertthat_0.2.1      Matrix_1.4-1         
##  [31] fastmap_1.1.0         lazyeval_0.2.2        cli_3.3.0            
##  [34] later_1.3.0           htmltools_0.5.3       tools_4.0.5          
##  [37] igraph_1.3.4          gtable_0.3.0          glue_1.6.2           
##  [40] RANN_2.6.1            reshape2_1.4.4        dplyr_1.0.9          
##  [43] Rcpp_1.0.9            scattermore_0.8       jquerylib_0.1.4      
##  [46] vctrs_0.4.1           nlme_3.1-155          progressr_0.10.0     
##  [49] lmtest_0.9-40         spatstat.random_2.2-0 xfun_0.31            
##  [52] stringr_1.4.0         globals_0.16.0        mime_0.12            
##  [55] miniUI_0.1.1.1        lifecycle_1.0.1       irlba_2.3.5          
##  [58] goftest_1.2-3         future_1.27.0         MASS_7.3-55          
##  [61] zoo_1.8-9             scales_1.1.1          spatstat.core_2.4-4  
##  [64] promises_1.2.0.1      spatstat.utils_2.3-1  parallel_4.0.5       
##  [67] RColorBrewer_1.1-2    yaml_2.3.5            reticulate_1.25      
##  [70] pbapply_1.5-0         gridExtra_2.3         sass_0.4.0           
##  [73] rpart_4.1.16          stringi_1.7.8         highr_0.9            
##  [76] rlang_1.0.4           pkgconfig_2.0.3       matrixStats_0.62.0   
##  [79] evaluate_0.15         lattice_0.20-45       tensor_1.5           
##  [82] ROCR_1.0-11           purrr_0.3.4           labeling_0.4.2       
##  [85] patchwork_1.1.1       htmlwidgets_1.5.4     tidyselect_1.1.2     
##  [88] parallelly_1.32.1     RcppAnnoy_0.0.19      plyr_1.8.7           
##  [91] magrittr_2.0.3        bookdown_0.24         R6_2.5.1             
##  [94] generics_0.1.3        DBI_1.1.3             withr_2.5.0          
##  [97] mgcv_1.8-39           pillar_1.8.0          fitdistrplus_1.1-8   
## [100] survival_3.3-1        abind_1.4-5           tibble_3.1.8         
## [103] future.apply_1.8.1    KernSmooth_2.23-20    utf8_1.2.2           
## [106] spatstat.geom_2.4-0   plotly_4.10.0         rmarkdown_2.13       
## [109] grid_4.0.5            data.table_1.14.2     digest_0.6.29        
## [112] xtable_1.8-4          tidyr_1.2.0           httpuv_1.6.5         
## [115] munsell_0.5.0         viridisLite_0.4.0     bslib_0.4.0